Tutorial on cp2k
Luca
Where can i find tutorial or guide for cp2k?
The examples in cp2k/tests/ and "CP2K input reference" command list
are very good but not enough for
new users.
Thanks
Teodoro Laino
unfortunately a tutorial is not still available. Then you may ask:
how can a new user approach cp2k?
Mainly with a great persistency and motivation ;-)
Having a look at the examples (take care that most of regtests have
parameters set in order to run fast and absolutely
have no sense for production runs), starting your own input and
asking to the google group for things that you don't really
understand or that look weird.
There's some sort pg plan for a tutorial but it will take some time..
Hope though these difficulties you will enjoy CP2K ;-)
Teo
Luca
I want to do:
1-Perform MM MD for protein in solution like NAMD or ORAC MD package.
2-Perform QM MD for molecules.
3-Perform QM/MM MD for enzyme. QM for active site.
and I hope....
4-"Metadynamics" for reaction coordinate in enzyme active site.
When i will do this I can write my notes
and make a pseudo-tutorial for cp2k users.
I hope in your aid.
Teodoro Laino
On 31 Aug 2007, at 14:45, Luca wrote:
>
> I understand ....like the installation :-)
Well if you managed already a successful installation you're beyond
the the top of the mountain ;-).. It's all downhill then ;-) LOL
>
> I want to do:
> 1-Perform MM MD for protein in solution like NAMD or ORAC MD package.
> 2-Perform QM MD for molecules.
> 3-Perform QM/MM MD for enzyme. QM for active site.
> and I hope....
> 4-"Metadynamics" for reaction coordinate in enzyme active site.
>
> When i will do this I can write my notes
> and make a pseudo-tutorial for cp2k users.
Great! That's what I think is a winning strategy.. I mean people
learning how to use cp2k and willing to share their knowledge with
the others!
maybe spending a couple of hours of their time writing good notes and
so on..
The Google Group was also created in order to allow this kind of
exchange more easily (uploading/downloading files and infos)..
> I hope in your aid.
>
No problem.. sure you can have my help!
teo
Axel
ciao luca,
On Aug 31, 8:45 am, Luca <bellucc...@unisi.it> wrote:
> I understand ....like the installation :-)
>
> I want to do:
> 1-Perform MM MD for protein in solution like NAMD or ORAC MD package.
> 2-Perform QM MD for molecules.
> 3-Perform QM/MM MD for enzyme. QM for active site.
> and I hope....
> 4-"Metadynamics" for reaction coordinate in enzyme active site.
>
> When i will do this I can write my notes
> and make a pseudo-tutorial for cp2k users.
> I hope in your aid.
in that case, i would suggest, that you start practicing with
one or two of the examples posted for the demo session of
our recent qm/mm workshop in philadelphia. see:
http://www.cmm.upenn.edu/qmmm2007.html
during trying out those we stumbled across a few useful
improvements of the cp2k code already, and since we have
already tried to set them up for different QM/MM code, they
would give a foundation for a future tutorial.
if i find a little more time over the weekend, i could add my
notes on making a biosystem work with cp2k for qm/mm to
the wiki-like part of this group.
there are also a few notes in the cvs on compiling and using
cp2k, that would be a good starting point for a tutorial and/or
user's guide.
cheers,
axel.
Teodoro Laino
If the final goal is to run QMMM simulations, starting directly with
QMMM simulations can be
quite difficult, most of the time impossible, and the risk is that
you may give up just because
the amount of things to learn at the same time (with no documentation
at all) is really massive.
This is a general rule obviously (not necessarily directed to Luca)..
depending on the personal
skills and motivation you may find that starting directly with QMMM
applies perfectly to your
learning curve for you.
In general what I suggest to people willing to try cp2k is to start
having some confidence in the
quantum package QS, maybe just trying to reproduce full quantum
results obtained with
other packages like GAMESS or MOLCAS or TURBOMOLE or your favourite
QM code..
At the same time is important to gain the same confidence in the
classical module FIST: running
small/medium systems already studied with other classical codes
(AMBER/CHARMM/NAMD/..)
Once one think to have enough control of both than QMMM comes naturally.
The idea is to learn step by step.. easier and more error proof.
Moreover, if you start QMMM simulations (with whatever package, not
necessarily cp2k) it is
necessary that you have some experience already on both quantum
simulation and classical
simulations.
The risk otherwise is to build new theories based on those
meaningless numbers
and see them published in the next number of SCIENCE or NATURE ;-)
LOL ..
teo
Axel
On Sep 1, 5:33 am, Teodoro Laino <teodoro.la...@gmail.com> wrote:
> May I just do a comment, about that, based on my experience?
> If the final goal is to run QMMM simulations, starting directly with
> QMMM simulations can be
> quite difficult, most of the time impossible, and the risk is that
> you may give up just because
> the amount of things to learn at the same time (with no documentation
> at all) is really massive.
point taken. i was actually thinking along those lines, i.e. that with
the ultimate goal of running qm/mm, the qm/mm input examples would
also make a good starting point for classical MD, too.
cheers,
axel.
Axel
on the same matter a question i was asked quite
a few times recently.
are there any plans to do a 'real' cp2k tutorial,
perhaps some time next year (early summer?).
with the currently increasing popularity (and usability!)
of cp2k, this may be a good time...
as a side effect, one would be 'forced' into collecting
useful tutorial material...
cheers,
axel.
Fawzi Mohamed
I think that it would be a great idea.
Indeed the tutorial in cp2k/doc/tutorial was created for a real
tutorial...
Fawzi
Axel
that is a bit difficult for 'normal' users to change and since i
believe
that users and not developers should write that kind of documentation
(corrected
by developers, of course), i'm currently in the process of re-writing
and
augmenting that document for the 'wiki' part of the forum here.
i'm encouraging everybody else here to participate and add their own
experiences and (hopefully) helpful comments. this is the best way to
acknowledge the effort of the developers. i'll make a more official
post once all of the existing material (from the cvs and my own
examples)
are available.
cheers,
axel.
> Fawzi
Fawzi Mohamed
On Sep 5, 2007, at 11:26 PM, Axel wrote:
> On Sep 5, 3:57 pm, Fawzi Mohamed <fa...@gmx.ch> wrote:
>> Indeed the tutorial in cp2k/doc/tutorial was created for a real
>> tutorial...
>
> that is a bit difficult for 'normal' users to change and since i
> believe
> that users and not developers should write that kind of documentation
> (corrected
> by developers, of course), i'm currently in the process of re-writing
> and
> augmenting that document for the 'wiki' part of the forum here.
great
> i'm encouraging everybody else here to participate and add their own
> experiences and (hopefully) helpful comments. this is the best way to
> acknowledge the effort of the developers. i'll make a more official
> post once all of the existing material (from the cvs and my own
> examples)
> are available.
looking forward to it
Fawzi